Natural Product: NPC262450

Natural Product IDNPC262450
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 AVIUTYMRHHBXPB-AIEDFZFUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 53384347
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey AVIUTYMRHHBXPB-AIEDFZFUSA-N
Standard InCHI InChI=1S/C15H20O8/c1-7(17)9-4-3-8(21-2)5-10(9)22-15-14(20)13(19)12(18)11(6-16)23-15/h3-5,11-16,18-20H,6H2,1-2H3/t11-,12+,13-,14-,15+/m0/s1
SMILES CC(=O)c1ccc(cc1O[C@H]1[C@H]([C@H]([C@@H]([C@H](CO)O1)O)O)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   328.12 Volume:   310.659
?
Van der Waals volume.
Dense:   1.056 LogP:   -0.284
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.202
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.151
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   13.0
TPSA:   125.68
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.511 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.424 Fsp3:   0.533
MCE-18:   51.522
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.49 Fluc inhibitor:   0.022
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.087
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.037
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.232 Promiscuous compounds:   0.165

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.029 MDCK Permeability:   -5.264
Pgp-inhibitor:   0.0 Pgp-substrate:   0.534
PAMPA:   0.998
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.961
20% Bioavailability (F20%):   0.881 30% Bioavailability (F30%):   0.901
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.858
Plasma Protein Binding (PPB):   66.943% Volume Distribution (VD):   0.148
Fu: 33.304%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.41
OATP1B3 inhibitor:   0.819 BCRP inhibitor:   0.038
BSEP inhibitor:   0.01

ADMET: Metabolism

CYP1A2-inhibitor:   0.529 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.007 CYP2C19-substrate:   0.005
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.584
HLM stability:   0.653
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  2.404 Half-life (T1/2):  2.496

ADMET: Toxicity

hERG Blockers:  0.032 hERG Blockers (10um):  0.158
Human Hepatotoxicity (H-HT):  0.652 Drug-induced Liver Injury (DILI):  0.836
AMES Toxicity:  0.931 Rat Oral Acute Toxicity:  0.07
Maximum Recommended Daily Dose:  0.023 Skin Sensitization:  0.983
Carcinogencity:  0.467 Eye Corrosion:  0.0
Eye Irritation:  0.641 Respiratory Toxicity:  0.12
Drug-induced Neurotoxicity:  0.175 Ototoxicity:  0.841
Hematotoxicity:  0.784 Drug-induced Nephrotoxicity:  0.856
Genotoxicity:  0.285 RPMI-8226 Immunitoxicity:  0.182
A549 Cytotoxicity:  0.41 Hek293 Cytotoxicity:  0.173
BCF:   0.257
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   2.736
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.129
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.296
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. PMID[11339628]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. bark n.a. PMID[17260795]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. Daejeon, Korea 2007-Jan PMID[19670875]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[20822014]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. root n.a. PMID[22547314]
NPO19352 Paeonia obovata Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[23497864]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota root bark Bozhou, Anhui Province, China 2010-AUG PMID[24377852]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. flower n.a. PMID[24504864]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota Flowers LuoYang, HeNan, China n.a. PMID[24621197]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19352 Paeonia obovata Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29741 Paeonia moutan Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29741 Paeonia moutan Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19352 Paeonia obovata Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19352 Paeonia obovata Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29741 Paeonia moutan Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19352 Paeonia obovata Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC262450 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC218685
0.7 Intermediate Similarity NPC294470
0.6909 Remote Similarity NPC23084
0.6471 Remote Similarity NPC217854
0.6393 Remote Similarity NPC479030
0.6349 Remote Similarity NPC213723
0.6308 Remote Similarity NPC23253
0.6275 Remote Similarity NPC276195
0.6275 Remote Similarity NPC212729
0.6275 Remote Similarity NPC604498
0.6154 Remote Similarity NPC269242
0.6111 Remote Similarity NPC60589
0.6111 Remote Similarity NPC469708
0.6111 Remote Similarity NPC609376
0.6038 Remote Similarity NPC153149
0.6034 Remote Similarity NPC479028
0.6034 Remote Similarity NPC479031
0.6 Remote Similarity NPC200092
0.5926 Remote Similarity NPC25817
0.5846 Remote Similarity NPC99233
0.5818 Remote Similarity NPC299144
0.5741 Remote Similarity NPC192810
0.5714 Remote Similarity NPC226712
0.5714 Remote Similarity NPC608788
0.5672 Remote Similarity NPC271479
0.5672 Remote Similarity NPC108674
0.5636 Remote Similarity NPC152722
0.5614 Remote Similarity NPC221090
0.5614 Remote Similarity NPC69513
0.5614 Remote Similarity NPC80098
0.5538 Remote Similarity NPC474044
0.5538 Remote Similarity NPC604892
0.5522 Remote Similarity NPC605700
0.5517 Remote Similarity NPC48863
0.5517 Remote Similarity NPC214454
0.5517 Remote Similarity NPC166040
0.5517 Remote Similarity NPC251981
0.5517 Remote Similarity NPC13745
0.5507 Remote Similarity NPC219163
0.5507 Remote Similarity NPC486379
0.55 Remote Similarity NPC270849
0.55 Remote Similarity NPC205054
0.55 Remote Similarity NPC604356
0.549 Remote Similarity NPC228907
0.5484 Remote Similarity NPC290069
0.5455 Remote Similarity NPC210192
0.5429 Remote Similarity NPC48640
0.5429 Remote Similarity NPC206378
0.5429 Remote Similarity NPC106625
0.5424 Remote Similarity NPC215833
0.541 Remote Similarity NPC26653
0.541 Remote Similarity NPC210478
0.5397 Remote Similarity NPC220560
0.5373 Remote Similarity NPC178851
0.537 Remote Similarity NPC142319
0.5362 Remote Similarity NPC76128
0.5345 Remote Similarity NPC145900
0.5333 Remote Similarity NPC49074
0.5323 Remote Similarity NPC479029
0.5294 Remote Similarity NPC30432
0.5294 Remote Similarity NPC606849
0.5286 Remote Similarity NPC61594
0.5278 Remote Similarity NPC300537
0.5254 Remote Similarity NPC95292
0.5246 Remote Similarity NPC472024
0.5246 Remote Similarity NPC251102
0.5246 Remote Similarity NPC162093
0.5246 Remote Similarity NPC210298
0.5246 Remote Similarity NPC606892
0.5238 Remote Similarity NPC106025
0.5231 Remote Similarity NPC294166
0.5231 Remote Similarity NPC115022
0.5211 Remote Similarity NPC56735
0.5211 Remote Similarity NPC147596
0.5205 Remote Similarity NPC473202
0.5167 Remote Similarity NPC40377
0.5167 Remote Similarity NPC310661
0.5167 Remote Similarity NPC9912
0.5161 Remote Similarity NPC26080
0.5161 Remote Similarity NPC80600
0.5161 Remote Similarity NPC165686
0.5156 Remote Similarity NPC232673
0.5156 Remote Similarity NPC97326
0.5156 Remote Similarity NPC34456
0.5147 Remote Similarity NPC177742
0.5143 Remote Similarity NPC308265
0.5135 Remote Similarity NPC93924
0.5079 Remote Similarity NPC248355
0.5077 Remote Similarity NPC199335
0.5077 Remote Similarity NPC146540
0.5077 Remote Similarity NPC477240
0.5075 Remote Similarity NPC146803
0.5068 Remote Similarity NPC607190

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC262450 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.5714 Remote Similarity NPD1091 Pre-clinical

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data